Project : WaddingtonMemory: Deciphering the role of regulatory factors driving epigenetic inheritance of alternative chromatin states

Epigenetics, the study of molecules and mechanisms that perpetuate alternative gene activity states in the context of the same DNA sequence, is a scientific field with many open questions that are highly relevant in biomedical sciences, ecology and evolution. Polycomb group proteins have been suggested to drive epigenetic inheritance. These proteins can repress transcription in multiple ways, including chromatin compaction, inhibition of the transcription machinery and higher-order chromatin organization and their dysregulation leads to cell fate changes and is associated with cancer, both in Drosophila and in mammals. Recently, we established a system that can drive reversible depletion of a protein of choice and discovered that a transient depletion of Polycomb proteins can drive the formation of tumors of epigenetic nature, i.e. in the absence of DNA mutations. We define them “Epigenetically Induced Cancers” or EICs (1).

The goal of the WaddingtonMemory project is to decipher how epigenetic components can lead to stable changes in cell fate, such as in the case of EICs, but also in mammalian systems. The project has three aims:

Aim 1: Identify the molecular steps leading to epigenetic cell fate derailment following transient Polycomb protein depletion in Drosophila.

·       Aim 1.1 will provide a deep multiomic description of epigenetically induced cancers, during a time-course of EICs induction. It will identify candidate EIC driver components.

·       Aim 1.2 will use cutting-edge imaging tools to study the candidates from Aim 1.1, identify cells-of-origin of EICs and higher-order chromosome folding changes associated to transformation.

Aim 2: Identify the Polycomb-targets leading to cell fate dysregulation and decipher their mechanistic role.

·       Aim 2.1 will identify transcription factors that are necessary and sufficient to initiate and/or maintain epigenetically induced cancers and reveal their downstream effects on chromatin and gene expression.

·       Aim 2.2 will analyze whether the disruption of higher-order nuclear organization of Polycomb proteins plays a role in EICs.

Aim 3: Test the role of epigenetic inheritance in mammalian cell differentiation. For this, we will focus on mouse gastruloids, an in vitro system that reflects cell differentiation events typically found in early embryogenesis.

·       Aim 3.1 will exploit transient protein depletion in gastruloid systems and profile their dynamic behavior, thanks to embryonic stem cell derivative lines that we have in the lab, that allow for reversible depletion of Polycomb components, or CTCF or to modulate histone acetylation.

·       Aim 3.2 will decipher mechanisms leading to epigenetic phenotypes in gastruloids, thanks to multiomics, imaging and functional perturbation of candidate components.

WaddingtonMemory has a transformative potential for the fields of epigenetics and cancer biology. It could redefine the role of epigenetic components in cancer and lead to novel therapeutic avenues